Publications

Here is a list of my academic publications and presentations. For a complete list of my work, please see my Google Scholar profile.

In all publications "*" denotes equal contribution.

Publications

PhenoBench: Mapping What a Deeply Phenotyped Human Cohort Can Tell Us

Gal Sapir, Alon Diament, Adva Wolf, Doron Yaya-Stupp, Dikla Gelbard Solodkin, Dana Azouri, Anat Etzion-Fuchs, Guy Lutsker, Eran Segal, Hagai Rossman. arXiv (Pre-print), September 2026

DOI PDF

Image-Conditioned Diffusion for Privacy-Preserving Synthetic Medical Images

Doron Yaya-Stupp, Guy Lutsker, Or Spiegel-Yerushalmi, Eran Segal. bioRxiv (Pre-print), May 2026

DOI PDF

Using generative AI to investigate medical imagery models and datasets

Oran Lang, Doron Yaya-Stupp, Ilana Traynis, Heather Cole-Lewis, Chloe R. Bennett, Courtney Lyles, Charles Lau, Michal Irani, Christopher Semturs, Dale R. Webster, Greg S. Corrado, Avinatan Hassidim, Yossi Matias, Yun Liu, Naama Hammel, Boris Babenko. EBioMedicine, January 2024

DOI PDF

Structured Understanding of Assessment and Plans in Clinical Documentation

Doron Stupp, Ronnie Barequet, I-Ching Lee, Eyal Oren, Amir Feder, Ayelet Benjamini, Avinatan Hassidim, Yossi Matias, Eran Ofek, Alvin Rajkomar. MedRxiv (Pre-print), April 2022

DOI PDF

Machine-learning of complex evolutionary signals improves classification of SNVs

Sapir Labes, Doron Stupp, Naama Wagner, Idit Bloch, Michal Lotem, Ephrat L. Lahad, Paz Polak, Tal Pupko, Yuval Tabach. NAR Genomics and Bioinformatics, January 2022

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CladeOScope: functional interactions through the prism of clade-wise co-evolution

Tomer Tsaban*, Doron Stupp*, Dana Sherill-Rofe, Idit Bloch, Ora Schueler-Furman, Reuven Wiener, Yuval Tabach. NAR Genomics and Bioinformatics, January 2021

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Co-evolution based machine-learning for predicting functional interactions between human genes

Doron Stupp, Elad Sharon, Idit Bloch, Marinka Zitnik, Or Zuk, Yuval Tabach. Nature Communications, January 2021

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Conservation Motifs – a novel evolutionary-based classification of proteins

Hodaya Beer, Dana Sherill-Rofe, Irene Unterman, Idit Bloch, Mendel Isseroff, Doron Stupp, Elad Sharon, Elad Zisman, Yuval Tabach. BioRxiv (Pre-print), January 2020

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Optimization of Co-evolution Analysis Through Phylogenetic Profiling Reveals Pathway-Specific Signals

Idit Bloch, Dana Sherill-Rofe, Doron Stupp, Irene Unterman, Hodaya Beer, Dolev Rahat, Elad Sharon, Yuval Tabach. Bioinformatics, January 2020

DOI PDF

A High-throughput Screening and computation Platform for Identifying Synthetic Promoters with Enhanced Cell-State Specificity (SPECS)

Ming-Ru Wu*, Lior Nissim*, Doron Stupp*, Erez Pery, Adina Binder-Nissim, Karen Weisinger, Sebastian Ricardo Palacios, Casper Enghuus, Melissa Humphrey, Zhizhuo Zhang, Eva Maria Novoa Pardo, Manolis Kellis, Ron Weiss, Samuel David Rabkin, Yuval Tabach, Timothy K. Lu. Nature Communications, January 2019

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Expanded CUG repeats trigger disease phenotype and expression changes through the RNAi machinery in C. elegans

Lena Qawasmi*, Maya Braun*, Irene Guberman, Emiliano Cohen, Lamis Naddaf, Anna Mellul, Olli Matilaine, Danielle share, Doron Stupp, Haya Chahine, Ehud Cohen, Susana Garcia, Yuval Tabach. Journal of Molecular Biology, January 2019

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Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy

Lior Nissim*, Ming-Ru Wu*, Erez Pery, Adina Binder-Nissim, Hiroshi I Suzuki, Doron Stupp, Claudia Wehrspaun, Yuval Tabach, Phillip A Sharp, Timothy K Lu. Cell, January 2017

DOI PDF

Presentations

Structured Understanding of Assessment and Plans in Clinical Documentation

Doron Stupp, Ronnie Barequet, I-Ching Lee, Eyal Oren, Amir Feder, Ayelet Benjamini, Avinatan Hassidim, Yossi Matias, Eran Ofek, Alvin Rajkomar. Presented as Poster, Lightning Talk at MLHC 2022, January 2022

Evolutionary Motifs – A Novel Way To Define Evolution Across A Thousand Of Species

Hodaya Beer, Dana Sherill-Rofe, Doron Stupp, Yuval Tabach. Presented as Poster at ISMB/ECCB 2019, January 2019

Machine Learning Based Phylogenetic Profiling (MLPP) - Using Local Co-Evolution for Functional Interaction Prediction and Uncovering Evolutionary Insights

Doron Stupp, Yuval Tabach. Presented as Poster, Oral Presentation at ISMB/ECCB 2019 and GGE 8 2019, January 2019

Publications

PhenoBench: Mapping What a Deeply Phenotyped Human Cohort Can Tell Us

Image-Conditioned Diffusion for Privacy-Preserving Synthetic Medical Images

Using generative AI to investigate medical imagery models and datasets

Structured Understanding of Assessment and Plans in Clinical Documentation

Machine-learning of complex evolutionary signals improves classification of SNVs

CladeOScope: functional interactions through the prism of clade-wise co-evolution

Co-evolution based machine-learning for predicting functional interactions between human genes

Conservation Motifs – a novel evolutionary-based classification of proteins

Optimization of Co-evolution Analysis Through Phylogenetic Profiling Reveals Pathway-Specific Signals

A High-throughput Screening and computation Platform for Identifying Synthetic Promoters with Enhanced Cell-State Specificity (SPECS)

Expanded CUG repeats trigger disease phenotype and expression changes through the RNAi machinery in C. elegans

Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy

Structured Understanding of Assessment and Plans in Clinical Documentation

Evolutionary Motifs – A Novel Way To Define Evolution Across A Thousand Of Species

Machine Learning Based Phylogenetic Profiling (MLPP) - Using Local Co-Evolution for Functional Interaction Prediction and Uncovering Evolutionary Insights

Predicting the Pathogenicity of Variants by Cross-Species Evolutionary Patterns Using Machine Learning

Solving Missing Heredity Syndromes via Genetic Algorithm Based Phylogenetic Profiling

Phylogenetic profiling for predicting PPI and interaction context using local co-evolution

Treatment of cutaneous leishmaniasis with daylight activated photodynamic therapy